In a part I am modeling there is a 3D sketch with a line that is coincident to a vertex. A ctrl Q force regen will cause this coincident relation to lose its reference. If I edit the sketch and repair the broken reference, it will break the next time the model does a regen. in other words, I can fix it, close the sketch, hit ctrl Q and it breaks immediately again. 

What type of things would cause SW to lose the internal IDs or any other information it needs to know what the sketch relations are? How would one try to find where the issue is?  And maybe most important, how would one make sure to avoid this in the future? 

Any help is appreciated